recipe pathogen-embed

Create reduced dimension embeddings for pathogen sequences

Homepage:

https://github.com/blab/pathogen-embed

License:

MIT / MIT

Recipe:

/pathogen-embed/meta.yaml

package pathogen-embed

versions:

3.1.0-0,  3.0.0-0,  2.3.0-0,  2.2.1-0,  2.2.0-1,  2.2.0-0,  2.1.0-0,  2.0.0-0

depends biopython:

>=1.83,<2

depends hdbscan:

>=0.8.36,<0.9.0

depends matplotlib-base:

>=3,<4

depends numba:

<0.59.0

depends numpy:

>=1.24.4,<2

depends pandas:

>=1.2.0,<2

depends python:

>=3.8

depends scikit-learn:

>=1.3,<1.5

depends umap-learn:

>=0.5.0,<0.6.0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pathogen-embed

and update with::

   mamba update pathogen-embed

To create a new environment, run:

mamba create --name myenvname pathogen-embed

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pathogen-embed:<tag>

(see `pathogen-embed/tags`_ for valid values for ``<tag>``)

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